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- PDB-8k8k: Structure of Klebsiella pneumonia ModA -

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Basic information

Entry
Database: PDB / ID: 8k8k
TitleStructure of Klebsiella pneumonia ModA
ComponentsMolybdate transporter periplasmic protein
KeywordsMETAL BINDING PROTEIN / Molybdate binding protein
Function / homologyMolybdate ABC transporter, substrate-binding protein / : / molybdate ion transport / Bacterial extracellular solute-binding protein / metal ion binding / Molybdate transporter periplasmic protein
Function and homology information
Biological speciesKlebsiella pneumoniae subsp. pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsZhao, Q. / Bartlam, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870053 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2023
Title: Structural analysis of molybdate binding protein ModA from Klebsiella pneumoniae.
Authors: Zhao, Q. / Su, X. / Wang, Y. / Liu, R. / Bartlam, M.
History
DepositionJul 31, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Molybdate transporter periplasmic protein


Theoretical massNumber of molelcules
Total (without water)27,0091
Polymers27,0091
Non-polymers00
Water3,783210
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.350, 69.747, 126.902
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Molybdate transporter periplasmic protein


Mass: 27008.760 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (strain HS11286) (bacteria)
Gene: KPHS_16010 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3GU89
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47.04 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 3
Details: 0.1 M Citric acid, 25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. obs: 17441 / % possible obs: 97.7 % / Redundancy: 6 % / Biso Wilson estimate: 21.84 Å2 / Rpim(I) all: 0.071 / Net I/σ(I): 12.8
Reflection shellResolution: 1.99→2.03 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 816 / Rpim(I) all: 0.195 / % possible all: 91.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→33.63 Å / SU ML: 0.1686 / Cross valid method: FREE R-VALUE / σ(F): 0.18 / Phase error: 21.3088
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2113 1669 10.09 %
Rwork0.1821 14866 -
obs0.185 16535 92.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.41 Å2
Refinement stepCycle: LAST / Resolution: 1.99→33.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1722 0 0 210 1932
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00731756
X-RAY DIFFRACTIONf_angle_d0.91682386
X-RAY DIFFRACTIONf_chiral_restr0.0584274
X-RAY DIFFRACTIONf_plane_restr0.0088308
X-RAY DIFFRACTIONf_dihedral_angle_d5.4411246
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.050.30461130.225974X-RAY DIFFRACTION74.05
2.05-2.120.22221270.21491122X-RAY DIFFRACTION86.98
2.12-2.190.24281340.18671185X-RAY DIFFRACTION88.52
2.2-2.280.23981200.20421060X-RAY DIFFRACTION81.66
2.28-2.390.2181370.18761221X-RAY DIFFRACTION90.78
2.39-2.510.23361430.18631278X-RAY DIFFRACTION96.8
2.51-2.670.24481400.19921275X-RAY DIFFRACTION96.32
2.67-2.880.24141420.19361288X-RAY DIFFRACTION95.14
2.88-3.160.22241500.18841341X-RAY DIFFRACTION99.2
3.17-3.620.19141510.17741342X-RAY DIFFRACTION99.01
3.62-4.560.17491510.15211343X-RAY DIFFRACTION98.16
4.56-33.630.19161610.17641437X-RAY DIFFRACTION97.26

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